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SSRL Headlines Vol. 7, No. 10  April, 2007


Contents of this Issue:

  1. Science Highlight — Revealing the Molecular Origins of Life
  2. Science Highlight — Closing in on Dangerous Infections
  3. Low Emittance Lattice for Brighter Beam
  4. Rapid Access Beam Time for SMB XAS BL7-3 — Online Application Now Available!
  5. New SSRL Faculty Chair and Vice-Chair Appointed
  6. Aaron Lindenberg Appointed to Faculty Position
  7. SSRL Users' Executive Committee Meeting
  8. Upcoming Schools, Users' Meetings and Workshops
  9. User Administration Update
  10. Photon Science Job Opportunities

1.  Science Highlight — Revealing the Molecular Origins of Life
       (contacts: M.P. Robertson,; W.G. Scott,

A close-up of the L1 ligase active site.
Researchers from the University of California, Santa Cruz, using macromolecular crystallography beam line 9-1 at SSRL have determined the three-dimensional structure of an RNA enzyme, or "ribozyme," that carries out a fundamental reaction required to make new RNA molecules. Their results provide insight into what may have been the first self-replicating molecule to arise billions of years ago on the evolutionary path toward the emergence of life. The findings are published in the March 16 issue of the journal Science.

William Scott and postdoctoral researcher Michael Robertson determined the structure of a ribozyme that joins two RNA subunits together in the same reaction that is carried out in biological systems by the protein known as RNA polymerase. The ribozyme used in the study is not an entirely self-replicating RNA molecule, but it does carry out the fundamental reaction required of such a molecule—a "ligase" reaction creating a bond between two RNA subunits.

The ribozyme has three stems that radiate from a central hub. The active site where ligation occurs is located on one stem, and the structure shows that the molecule folds in such a way that parts of another stem are positioned over the ligation site, forming a pocket where the reaction takes place. A magnesium ion bound to one stem and positioned in the pocket plays an important role in the reaction, Robertson said.

To learn more about this research see the full scientific highlight at:

2.  Science Highlight — Closing in on Dangerous Infections
      (contacts: L. Craig,; J.A. Tainer,

pilin figure
A team of researchers working at SSRL has determined the atomic structure of an assemblage of fiber-forming proteins found in the cell membranes of many dangerous types of bacteria. The protein, called pilin, assembles into filamentous organelles called Type IV pili found on the surfaces of most Gram-negative bacteria. Type IV pili plays a central role in how these bacterial pathogens infect a host and are involved in cellular functions such as motility, adhesion, microcolony formation and uptake of DNA and specific filamentous phage.

John Tainer and colleagues at The Scripps Research Institute succeeded in solving the crystal structures of T4P from several important human pathogens using the macromolecular crystallography beam lines at SSRL (BLs 7-1, 9-1, 9-2 and 11-1). Membrane proteins are notoriously difficult to crystallize, and fiber-forming proteins were actually once declared "uncrystallizable" by the eminent x-ray crystallographer Sir Lawrence Bragg.

The prominent exposure of T4P on bacterial surfaces and their key functions in virulence make T4P attractive targets for vaccines and therapeutics. Detailing the molecular structure of T4P will greatly benefit the design of drugs that target these structures.

To learn more about this research see the full scientific highlight at:

3.   Low Emittance Lattice for Brighter Beam
      (contacts: J. Safranek,; R. Hettel,

The SSRL Accelerator Physics group has utilized a number of recent machine physics blocks to test injection and stored current operations of the SPEAR3 accelerator in a low emittance mode. Tests of this new magnetic lattice, which lowers the SPEAR3 emittance from 15nm*rad to 9.75nm*rad, proved highly successful. Consequently, initial low emittance user operations will commence in early May. In this mode of operations the electron beam horizontal size shrinks approximately 20%, resulting in a commensurate reduction in the horizontal spot size on most focused end stations. To preserve the stored electron beam lifetime, the ring vertical coupling is increased somewhat. This results in slightly larger electron beam vertical size, but the increase is sufficiently small that the effect on focused beam vertical size is not observable.

4.   Rapid Access Beam Time for SMB XAS BL7-3 — Online Application Now Available!

      (contact: S. DeBeer George,

SMB BL Instrumentation
Beginning in May, a new rapid access proposal mechanism for biological x-ray absorption spectroscopy (XAS) will be implemented on SSRL BL7-3. A block of 6 shifts of beam time will be set aside each month for rapid access user runs. This time will allow new and current biological XAS users to perform feasibility tests. Allocation of time will be based on a one-page scientific proposal, which will be reviewed by the SMB subpanel of the PRP. Rapid access proposal should be submitted by the first of each month, and users will be notified ~2 weeks prior to their allocated beam time. New users scheduled for beam time under a rapid access proposal will be trained by SSRL staff. Staff will provide training on all aspects of the experimental setup (beam line optics, use of detectors, data collection software) and will also advise users on sample preparation and data analysis. This will help new users efficiently utilize their beam time, and prepare them for successful future experiments. The rapid access proposal process should also benefit existing biological XAS users, allowing a mechanism for testing new ideas outside existing proposals.

To apply for rapid access time, please fill out the application form at:  For questions, please contact Serena DeBeer George (

5.  New SSRL Faculty Chair and Vice-Chair Appointed
      (contact: K.O. Hodgson,

P.Bucksbaum P. Bucksbaum
B. Hedman
On April 1, Phil Bucksbaum was appointed the new Chairperson of the SSRL Faculty and Britt Hedman the new Vice-Chair. The position of Vice-Chair has just been created, recognizing the increasing scope and scale of activities as faculty programs expand in the coming years. With this change, Gordon Brown, Jr. completed a 9-year tenure as Faculty Chairperson, during which the Faculty has significantly expanded in number, and new scientific directions have evolved. A new Faculty Development Plan was also developed under his leadership. The new Plan provides a strong platform for future development in Photon Science at SLAC/Stanford University and the role of the Faculty. Also as a part of the transition, an SSRL Faculty Affairs Office has been created with Amy Rutherford as administrator and coordinator. The process of changing the name of the SSRL Faculty to the Photon Science Faculty is in the final stage and is expected to become official soon. Information about the SSRL faculty is found at:

6.   Aaron Lindenberg Appointed to Faculty Position
      (contact: J. Stöhr,

Lindenberg pic
A. Lindenberg
It is a pleasure to announce that Aaron Lindenberg has accepted a joint faculty position in the Photon Science Department at SLAC and the Materials Science and Engineering (MSE) Department in the School of Engineering at Stanford. Aaron received his Ph.D. in the Physics Department at UC Berkeley and was previously a staff member in the PULSE Center at SLAC. He played an important role in the ultrafast experiments performed at the Sub-Picoscecond Photon Source (SPPS). His expertise in materials science and ultrafast techniques will strengthen the scientific programs of both PULSE and XLAM and foster links to the MSE Department. At SSRL we are excited to have Aaron as a user and are also looking forward to his involvement with the LCLS.

7.   SSRL Users' Executive Committee Meeting

      (contact: C.S. Kim (Chair),

The SSRL Users' Organization Executive Committee (SSRLUOEC) met on Monday, April 23. Several topics were discussed including a follow up to the users' survey which was conducted in January, an update on user advocacy activities by the Synchrotron and Neutron Users' Group (SNUG), plans for the joint SSRL and LCLS annual users' meeting and workshops, accelerator and low emittance optics developments, and undergraduate research incentives. Representatives from the SLAC Director Search Committee attended part of the meeting to encourage users to participate in the search process for the next Director; Jonathan Dorfan announced recently that he will step down as SLAC Director later this year. In conjunction with the search committee, the SSRLUOEC developed a brief survey and is soliciting user input by May 1 into the opportunities and challenges facing the lab in the next decade, the attributes of the next director, and names of potential candidates.

Representatives from the Stanford Guest House also participated in part of the SSRLUOEC meeting to provide an update on the Guest House. In May all of the bunk bed rooms will be converted to double bed rooms, and many of the queen bed rooms will be converted to two double bed rooms as these are the most requested room type. Several upgrades to the Guest House were made recently including new linens and upgraded bath products, the addition of hairdryers, bicycles available for rent, and more frequent shuttle service to Stanford (every 20 minutes). SSRL and SLAC guests will continue to receive a discount for rooms ($75 vs. $89 for one double bed; $105 vs. $119 for a queen or two double beds).

The Guest House acknowledged that at times it is difficult to accommodate users when there are major events occurring at SLAC or Stanford, but overall, the occupancy rates are not as high as desired. On some occasions when we anticipate a shortage of rooms (such as during the June 14-21 Stanford graduation), we reserve a group block for SSRL users. When seeking reservations, specify your SSRL affiliation to receive the discounted rates and to determine if there are any SSRL rooms available. Users who have questions or experience any problems related to the Guest House are encouraged to contact Group Coordinator Kristi Nelson at 650-926-5193 or Guest House Manager Jonathan Faulkner.

8.   Upcoming Schools, Users' Meetings and Workshops

Ultrafast Summer School Poster
2007 Ultrafast Summer School Website
At Other DOE Light Sources

9.   User Administration Update
      (contact: C. Knotts,

Proposal Submittal: X-ray/VUV proposals are due by May 1. Proposals received by this date will be peer reviewed and eligible for beam time beginning in November 2007. Rapid access and letter of intent proposals can be submitted at any time.

July 1, 2007 is the next deadline for submitting macromolecular crystallography proposals. For beam time before fall 2007, please submit a Rapid Access proposal or contact L. Dunn ( for more information.

Materials Diffraction Beam Time Available: We are currently accepting beam time requests for materials science diffraction experiments on SSRL BL11-3. Users interested in requesting beam time on BL11-3 through the end of the current run on August 6 should submit a request using the electronic form at:

10.   Photon Science Job Opportunities

A number of positions are currently available at SSRL and LUSI. Please refer to the Photon Science Job Openings page for more information about these job opportunities.


SSRL Headlines is published electronically monthly to inform SSRL users, sponsors and other interested people about happenings at SSRL. SSRL is a national synchrotron user facility operated by Stanford University for the U.S. Department of Energy Office of Basic Energy Sciences. Additional support for the structural biology program is provided by the DOE Office of Biological and Environmental Research, the NIH National Center for Research Resources and the NIH Institute for General Medical Sciences. Additional information about SSRL and its operation and schedules is available from the SSRL WWW site.


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Last Updated: 30 APR 2007
Content Owner: L. Dunn
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